Chlorine in PDB 5fdr: Mcl-1 Complexed with Small Molecule Inhibitor

The structure of Mcl-1 Complexed with Small Molecule Inhibitor, PDB code: 5fdr was solved by B.Zhao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.75 / 2.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	35.040, 115.005, 95.327, 90.00, 91.17, 90.00
R / Rfree (%)	22.4 / 28.3

The binding sites of Chlorine atom in the Mcl-1 Complexed with Small Molecule Inhibitor (pdb code 5fdr). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Mcl-1 Complexed with Small Molecule Inhibitor, PDB code: 5fdr:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in the Mcl-1 Complexed with Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Mcl-1 Complexed with Small Molecule Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl400 b:24.8 occ:1.00 CL2 A:5X3400 0.0 24.8 1.0 C17 A:5X3400 1.8 23.9 1.0 C16 A:5X3400 2.7 21.0 1.0 C19 A:5X3400 2.7 24.3 1.0 C20 A:5X3400 3.0 30.6 1.0 O A:ALA227 3.1 35.5 1.0 C A:ALA227 3.3 33.9 1.0 CB A:MET231 3.4 21.5 1.0 C25 A:5X3400 3.4 36.5 1.0 CD1 A:PHE228 3.4 18.6 1.0 C26 A:5X3400 3.5 38.0 1.0 N A:PHE228 3.7 20.6 1.0 CA A:PHE228 3.8 33.4 1.0 CB A:ALA227 3.8 22.8 1.0 CE1 A:PHE228 3.9 21.9 1.0 CG A:MET231 3.9 30.5 1.0 C21 A:5X3400 4.0 34.0 1.0 C15 A:5X3400 4.0 22.7 1.0 C13 A:5X3400 4.1 32.1 1.0 CA A:ALA227 4.1 32.8 1.0 N24 A:5X3400 4.3 33.8 1.0 CE A:MET231 4.5 45.2 1.0 CG A:PHE228 4.5 27.0 1.0 N23 A:5X3400 4.6 21.1 1.0 C14 A:5X3400 4.6 26.5 1.0 CA A:MET231 4.7 35.0 1.0 C A:PHE228 4.7 34.8 1.0 N A:MET231 4.7 27.2 1.0 C22 A:5X3400 4.7 40.3 1.0 O A:PHE228 4.8 44.8 1.0 CB A:PHE228 4.8 27.4 1.0 CD1 A:PHE270 4.8 42.0 1.0 CE1 A:PHE270 4.9 30.4 1.0

Chlorine binding site 2 out of 8 in the Mcl-1 Complexed with Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Mcl-1 Complexed with Small Molecule Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl400 b:25.7 occ:1.00 CL A:5X3400 0.0 25.7 1.0 C39 A:5X3400 1.8 29.7 1.0 C34 A:5X3400 2.7 28.3 1.0 C37 A:5X3400 2.8 17.8 1.0 C35 A:5X3400 3.0 25.8 1.0 C38 A:5X3400 3.1 11.5 1.0 CE2 A:PHE270 3.7 24.6 1.0 CE A:MET250 3.8 35.6 1.0 C33 A:5X3400 4.0 17.4 1.0 C36 A:5X3400 4.0 17.3 1.0 CB A:LEU246 4.1 37.1 1.0 CD2 A:PHE270 4.1 25.6 1.0 CD2 A:LEU246 4.2 47.2 1.0 CD1 A:LEU246 4.3 43.2 1.0 CG A:LEU246 4.4 41.6 1.0 CD1 A:LEU235 4.5 45.0 1.0 CB A:MET250 4.5 22.6 1.0 C32 A:5X3400 4.5 25.8 1.0 CG2 A:VAL274 4.6 16.1 1.0 CG A:MET250 4.8 35.4 1.0 CZ A:PHE270 4.8 26.0 1.0 O A:LEU246 4.9 47.0 1.0

Chlorine binding site 3 out of 8 in the Mcl-1 Complexed with Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Mcl-1 Complexed with Small Molecule Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl400 b:27.6 occ:1.00 CL2 B:5X3400 0.0 27.6 1.0 C17 B:5X3400 1.8 20.6 1.0 C19 B:5X3400 2.7 24.4 1.0 C16 B:5X3400 2.7 21.3 1.0 C20 B:5X3400 3.1 21.5 1.0 O B:ALA227 3.2 29.3 1.0 CB B:MET231 3.3 23.2 1.0 C21 B:5X3400 3.4 17.9 1.0 C22 B:5X3400 3.4 25.9 1.0 C B:ALA227 3.5 30.2 1.0 CG B:MET231 3.6 28.0 1.0 CD2 B:PHE228 3.7 23.2 1.0 N B:PHE228 3.9 27.3 1.0 CA B:PHE228 4.0 37.4 1.0 C13 B:5X3400 4.0 34.8 1.0 CB B:ALA227 4.0 29.3 1.0 C15 B:5X3400 4.0 19.5 1.0 C25 B:5X3400 4.1 18.6 1.0 CE2 B:PHE228 4.3 22.5 1.0 CA B:ALA227 4.3 30.0 1.0 N23 B:5X3400 4.4 26.8 1.0 CE B:MET231 4.5 52.8 1.0 C14 B:5X3400 4.5 32.5 1.0 CA B:MET231 4.7 24.8 1.0 N24 B:5X3400 4.7 28.3 1.0 CG B:PHE228 4.8 24.3 1.0 N B:MET231 4.9 26.8 1.0 CE1 B:PHE270 4.9 33.7 1.0 SD B:MET231 4.9 47.2 1.0 C B:PHE228 4.9 28.2 1.0 CD1 B:PHE270 4.9 26.4 1.0

Chlorine binding site 4 out of 8 in the Mcl-1 Complexed with Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Mcl-1 Complexed with Small Molecule Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl400 b:49.7 occ:1.00 CL B:5X3400 0.0 49.7 1.0 C39 B:5X3400 1.8 41.4 1.0 C37 B:5X3400 2.7 30.0 1.0 C34 B:5X3400 2.8 28.6 1.0 C38 B:5X3400 3.0 16.3 1.0 C35 B:5X3400 3.2 29.1 1.0 CD2 B:LEU246 3.8 36.5 1.0 CE2 B:PHE270 3.8 27.9 1.0 CD1 B:LEU246 3.9 37.6 1.0 C33 B:5X3400 4.0 24.8 1.0 C36 B:5X3400 4.0 25.7 1.0 CB B:LEU246 4.1 26.1 1.0 CG B:LEU246 4.1 36.2 1.0 CD1 B:LEU235 4.1 41.2 1.0 CD2 B:PHE270 4.2 26.6 1.0 SD B:MET250 4.3 42.3 1.0 CB B:MET250 4.5 17.5 1.0 C32 B:5X3400 4.6 34.2 1.0 CG B:MET250 4.8 30.9 1.0 CZ B:PHE270 4.8 37.8 1.0 O B:LEU246 5.0 42.2 1.0

Chlorine binding site 5 out of 8 in the Mcl-1 Complexed with Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Mcl-1 Complexed with Small Molecule Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl400 b:60.6 occ:1.00 CL2 C:5X3400 0.0 60.6 1.0 C17 C:5X3400 1.8 57.4 1.0 C19 C:5X3400 2.7 34.6 1.0 C16 C:5X3400 2.8 38.0 1.0 C20 C:5X3400 3.0 30.9 1.0 O C:ALA227 3.3 28.1 1.0 C25 C:5X3400 3.3 32.1 1.0 CB C:MET231 3.5 23.1 1.0 C26 C:5X3400 3.5 30.7 1.0 CD1 C:PHE228 3.5 21.4 1.0 C C:ALA227 3.5 25.5 1.0 N C:PHE228 3.8 24.1 1.0 C21 C:5X3400 3.8 16.4 1.0 CA C:PHE228 3.9 31.7 1.0 CG C:MET231 3.9 39.9 1.0 CE1 C:PHE228 4.0 22.3 1.0 C13 C:5X3400 4.1 30.2 1.0 C15 C:5X3400 4.1 20.5 1.0 CB C:ALA227 4.1 25.2 1.0 N24 C:5X3400 4.2 21.8 1.0 CA C:ALA227 4.4 25.4 1.0 N23 C:5X3400 4.4 21.6 1.0 C14 C:5X3400 4.6 29.6 1.0 C22 C:5X3400 4.6 9.2 1.0 CG C:PHE228 4.7 22.7 1.0 CE1 C:PHE270 4.7 35.0 1.0 C C:PHE228 4.8 32.4 1.0 CD1 C:PHE270 4.8 36.6 1.0 CA C:MET231 4.8 29.8 1.0 O C:PHE228 4.8 23.0 1.0 CE C:MET231 4.8 45.8 1.0 CB C:PHE228 4.9 29.1 1.0 N C:MET231 4.9 37.8 1.0

Chlorine binding site 6 out of 8 in the Mcl-1 Complexed with Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Mcl-1 Complexed with Small Molecule Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl400 b:28.6 occ:1.00 CL C:5X3400 0.0 28.6 1.0 C39 C:5X3400 1.8 18.8 1.0 C37 C:5X3400 2.7 17.1 1.0 C34 C:5X3400 2.7 22.9 1.0 C38 C:5X3400 2.9 14.7 1.0 C35 C:5X3400 3.0 17.6 1.0 CD2 C:LEU246 3.8 28.4 1.0 CE2 C:PHE270 3.9 25.0 1.0 CE C:MET250 3.9 37.1 1.0 C33 C:5X3400 4.0 26.9 1.0 C36 C:5X3400 4.0 30.7 1.0 CB C:LEU246 4.1 33.1 1.0 CD1 C:LEU235 4.1 21.1 1.0 CD2 C:PHE270 4.2 20.9 1.0 CD1 C:LEU246 4.2 36.5 1.0 CG C:LEU246 4.3 36.7 1.0 CB C:MET250 4.5 28.9 1.0 C32 C:5X3400 4.5 31.2 1.0 CG C:MET250 4.7 40.9 1.0 CG2 C:VAL274 4.7 33.9 1.0 O C:LEU246 4.9 39.6 1.0 CD1 C:LEU290 5.0 19.4 1.0

Chlorine binding site 7 out of 8 in the Mcl-1 Complexed with Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Mcl-1 Complexed with Small Molecule Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl400 b:63.5 occ:1.00 CL2 D:5X3400 0.0 63.5 1.0 C17 D:5X3400 1.8 45.0 1.0 C19 D:5X3400 2.7 42.7 1.0 C16 D:5X3400 2.8 37.4 1.0 C20 D:5X3400 3.0 34.6 1.0 O D:ALA227 3.1 23.5 1.0 C21 D:5X3400 3.3 30.4 1.0 CB D:MET231 3.4 24.1 1.0 C D:ALA227 3.4 25.9 1.0 C22 D:5X3400 3.4 28.9 1.0 CD1 D:PHE228 3.6 31.8 1.0 CA D:PHE228 3.7 29.4 1.0 N D:PHE228 3.7 24.8 1.0 CG D:MET231 3.8 36.5 1.0 C25 D:5X3400 3.9 12.8 1.0 C13 D:5X3400 4.0 41.7 1.0 C15 D:5X3400 4.1 27.4 1.0 CB D:ALA227 4.1 19.1 1.0 CE1 D:PHE228 4.2 32.7 1.0 N23 D:5X3400 4.2 22.8 1.0 CE2 D:PHE270 4.3 38.1 1.0 CA D:ALA227 4.3 30.9 1.0 CD2 D:PHE270 4.4 41.0 1.0 N24 D:5X3400 4.5 23.3 1.0 C D:PHE228 4.6 38.1 1.0 O D:PHE228 4.6 44.6 1.0 C14 D:5X3400 4.6 33.3 1.0 CG D:PHE228 4.6 21.8 1.0 SD D:MET231 4.7 66.8 1.0 CB D:PHE228 4.7 22.8 1.0 CA D:MET231 4.7 34.1 1.0 C26 D:5X3400 4.8 0.2 1.0 CZ D:PHE270 4.8 31.3 1.0 N D:MET231 4.9 33.0 1.0

Chlorine binding site 8 out of 8 in the Mcl-1 Complexed with Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Mcl-1 Complexed with Small Molecule Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl400 b:60.0 occ:1.00 CL D:5X3400 0.0 60.0 1.0 C39 D:5X3400 1.8 44.5 1.0 C34 D:5X3400 2.7 42.5 1.0 C37 D:5X3400 2.8 18.8 1.0 C35 D:5X3400 3.0 37.2 1.0 C38 D:5X3400 3.1 7.7 1.0 CD1 D:LEU246 3.8 31.2 1.0 CE1 D:PHE270 3.9 24.0 1.0 C33 D:5X3400 4.0 34.2 1.0 C36 D:5X3400 4.0 21.7 1.0 CD2 D:LEU246 4.1 29.7 1.0 CB D:LEU246 4.1 26.5 1.0 CD1 D:PHE270 4.2 22.8 1.0 CG D:LEU246 4.3 27.7 1.0 SD D:MET250 4.4 41.3 1.0 CD1 D:LEU235 4.4 27.7 1.0 C32 D:5X3400 4.5 29.9 1.0 CB D:MET250 4.6 23.3 1.0 O D:LEU246 4.7 38.7 1.0 CG2 D:VAL274 4.9 34.5 1.0 CG D:MET250 4.9 31.0 1.0

N.F.Pelz, Z.Bian, B.Zhao, S.Shaw, J.C.Tarr, J.Belmar, C.Gregg, D.V.Camper, C.M.Goodwin, A.L.Arnold, J.L.Sensintaffar, A.Friberg, O.W.Rossanese, T.Lee, E.T.Olejniczak, S.W.Fesik. Discovery of 2-Indole-Acylsulfonamide Myeloid Cell Leukemia 1 (Mcl-1) Inhibitors Using Fragment-Based Methods. J.Med.Chem. V. 59 2054 2016.
ISSN: ISSN 0022-2623
PubMed: 26878343
DOI: 10.1021/ACS.JMEDCHEM.5B01660